SNP and Haplotype-Based Genomic Selection of Quantitative Traits in Eucalyptus globulus
SNP and Haplotype-Based Genomic Selection of Quantitative Traits in Eucalyptus globulus
复制标题
DOI：
10.3390/plants8090331
复制
发表时间：
2019-09-01
期刊：
影响因子：
4.5
通讯作者：
Mora, Freddy
中科院分区：
文献类型：
--
作者：
Ballesta, Paulina;Maldonado, Carlos;Mora, Freddy
蓝桉(Labill.)是温带和亚热带地区最重要的栽培桉树之一，已成功进行集约育种。在这项研究中，评估了包含单倍型和单核苷酸多态性 (SNP) 影响的贝叶斯基因组模型，以预测 6 年生育种群体中与木材质量和树木生长相关的数量性状。为此，考虑了以下标记：(a) 与 14 K SNP 标记 (SNP) 相似，(b) 与 3 K 单倍型 (HAP) 相似，以及 (c) 未分配给单倍型的单倍型和 SNP (HAP-SNP)。预测能力值（PA）取决于基因组预测模型和标记。平均而言，贝叶斯岭回归 (BRR) 和贝叶斯 C 对于大多数性状具有最高的 PA。值得注意的是，包含单倍型效应（HAP 或 HAP-SNP）的基因组模型显着增加了低遗传力性状的 PA。例如，基于 HAP 的 BRR 具有最高的阀杆直线度 PA (0.58)。一致的是，基因组模型的遗传力估计高于这些性状的基于谱系的估计。这些结果为在桉树育种计划中实施基因组选择提供了额外的视角，这对于改善低遗传力的性状特别有益。
Eucalyptus globulus (Labill.) is one of the most important cultivated eucalypts in temperate and subtropical regions and has been successfully subjected to intensive breeding. In this study, Bayesian genomic models that include the effects of haplotype and single nucleotide polymorphisms (SNP) were assessed to predict quantitative traits related to wood quality and tree growth in a 6-year-old breeding population. To this end, the following markers were considered: (a) similar to 14 K SNP markers (SNP), (b) similar to 3 K haplotypes (HAP), and (c) haplotypes and SNPs that were not assigned to a haplotype (HAP-SNP). Predictive ability values (PA) were dependent on the genomic prediction models and markers. On average, Bayesian ridge regression (BRR) and Bayes C had the highest PA for the majority of traits. Notably, genomic models that included the haplotype effect (either HAP or HAP-SNP) significantly increased the PA of low-heritability traits. For instance, BRR based on HAP had the highest PA (0.58) for stem straightness. Consistently, the heritability estimates from genomic models were higher than the pedigree-based estimates for these traits. The results provide additional perspectives for the implementation of genomic selection in Eucalyptus breeding programs, which could be especially beneficial for improving traits with low heritability.